EMBOSS: Project Meeting (Mon 1st Aug 11)

Attendees

1. Minutes of the last meeting

2. Maintenance etc.

2.1 Applications

Peter is testing the impact of restricting qualifiers to unique
names that are not a short form of another qualifier. It appears that
the code only compares to earlier qualifiers in the ACD file. The
tests will be run again with a comparison against all qualifiers.

Peter reported that a user has offered to help update the
isoelectric point calculations by requesting data values from ExPASy
and will try updating the code.

Jon is updating the one-line descriptions in ACD files to make
the grammar consistent.

Alan has reported fixing the tcode scoring bug which was
caused by a missing line the the data file.

2.2 Libraries

Peter fixed an issue with using PCRE regular expressions to
extract very long translations in GFF format. The regular expression
hung (or took a very long time) when checking for a long quoted string
with possible escaped quotes. The revised code first replaces escaped
quotes with another character, then extracts the string and if
necessary reinserts the escaped quotes.

Peter and Jon have revised the generated library
documentation. Redundant lines have been removed, as have lines which
only repeat a standard text. The lists of datatypes, sections and
functions have been made into bulleted lists which are easier to
read. For each function, the initial release number has been added by
inspecting past releases.

Peter will review the book sections on handling datatypes to
see how much of them could be automatically generated.

Michael noted that the functions for memory checking are called
ajMemCheck and ajMemProbe but the configuration test is for
HAVE_MCHECK. Peter will check on this and consider renaming the
option, but as the GNU library function is called mcheck it may remain
unchanged.

Michael noted that the symbols and enumerations in libraries
are not documented and some globally available enumerations could be
renamed for consistency and to avoid possible clashed with
non-EMBOSS names.

2.3 Configuration

Michael is trying to clean up the main configure file.

The Makefile for the AJAX ensembl library has been cleaned up to use
only direct dependencies. Alan is checking the modified files.
The aim is to have library links only where they are needed, for
example PostGres and MySQL are currently only used in the ajax/core
library and are not needed in the CFLAGS for other libraries.

The X11 library location test for MacOSX is probably no longer needed.

2.4 Other

Peter has split QA tests so that each EMBASSY package has its
own test/qatest.dat file. The qatest.pl script searches
for all qatest.dat files. In EMBASSY packages where there are files
generated by another package for use in a test, the other tests are
imported under new names with new "AX" and "AY" line types for the
application and package name.

Peter has been replying to discussions about licensing of data
files on the EMBOSS and Debian mailing lists. DebianMed developers are
concerned that swissprot example files have a license that forbids
changing Swissprot without permission. Peter pointed out that
while this is not a serious issue, DebianMed need to consider how
they handle the licensing of GO and other data files. Other Open-Bio
projects have pointed out similar issues.

Michael noted that the licensing information in the source files
still refers to the old name of "GNU Library GPL". All files should
be updated to "Lesser" which is now the official name.

Header files should also have the license information as this is
often the first place developers will look.

We should also consider an @source documentation block in header
files.

3. New developments

3.1 Reference sequences

3.2 Support for interfaces and GUIs

3.3 Data access

4. Administration

5. Documentation and Training

5.1 Web server

Peter would like to replace the home page with a new style that
better indicated the documentation, news, mailing lists and other
information. BioPython's home page is a good example, but is wiki
based.

5.2 Books

Jon has updated the user manual with corrections from the
original proofs.

Peter has updated the version numbers and some examples in all 3
books so that the web pages and original XML match release 6.4.0.

For the book text Peter suggested we should use names for the
pages rather than chapter and section so that we can link permanently
to, for example, functions handling translations.

6. User queries and answers

All done.

Peter is working through the remaining items on the bug
tracker list. Most were already resolved. None were serious bugs. Less
than 20 items remain.